The polarized distribution of poly(A+)-mRNA-induced functional ion channels in the Xenopus oocyte plasma membrane is prevented by anticytoskeletal drugs

Foreign mRNA was expressed in Xenopus laevis oocytes. Newly expressed ion currents localized in defined plasma membrane areas were measured using the two-electrode voltage clamp technique in combination with a specially designed chamber, that exposed only part of the surface on the oocytes to channel agonists or inhibitors. Newly expressed currents were found to be unequally distributed in the surface membrane of the oocyte. This asymmetry was most pronounced during the early phase of expression, when channels could almost exclusively be detected in the animal hemisphere of the oocyte. 4 d after injection of the mRNA, or later, channels could be found at a threefold higher density at the animal than at the vegetal pole area. The pattern of distribution was observed to be similar with various ion channels expressed from crude tissue mRNA and from cRNAs coding for rat GABAA receptor channel subunits. Electron microscopical analysis revealed very similar microvilli patterns at both oocyte pole areas. Thus, the asymmetric current distribution is not due to asymmetric surface structure. Upon incubation during the expression period in either colchicine or cytochalasin D, the current density was found to be equal in both pole areas. The inactive control substance beta-lumicolchicine had no effect on the asymmetry of distribution. Colchicine was without effect on the amplitude of the expressed whole cell current. Our measurements reveal a pathway for plasma membrane protein expression endogenous to the Xenopus oocyte, that may contribute to the formation and maintenance of polarity of this highly organized cell.

LINKAGE RELATIONSHIPS AMONG PROTEIN-CODING LOCI IN FISHES OF THE GENUS XIPHOPHORUS

Inbred strains of three species of fishes of the genus Xiphophorus (platyfish and swordtails) were crossed to produce intra- and interspecific F(,1) hybrids, which were then backcrossed to one or both parental stocks. Backcross hybrids were used for the analysis of segregation and linkage of 33 protein-coding loci (whose products were visualized by starch gel electrophoresis) and a sex-linked pigment pattern gene. Segregation was Mendelian for all loci with the exception of one instance of segregation distortion. Six linkage groups of enzyme-coding loci were established: LG I, ADA --6%-- G(,6)PD --24%-- 6PGD; LG II, Est-2 --27%-- Est-3 --0%-- Est-5 --23%-- LDH-1 --16%-- MPI; LG III, AcPh --38%-- G(,3)PD-1 (GUK-2 --14%-- G(,3)PD-1 is also in LG III, but the position of GUK-2 with respect to AcPh has not yet been determined); LG IV, GPI-1 --41%-- IDH-1; LG V, Est-1 --38%-- MDH-2; and LG VI, P1P --7%-- UMPK-1 (P1P is a plasma protein, very probably transferrin).^ Sex-specific recombination appeared absent in LG II and LG IV locus pairs; significantly higher male recombination was demonstrated in LG I but significantly higher female recombination was detected in LG V. Only one significant population-specific difference in recombination was detected, in the G(,6)PD - 6PGD region of LG I; the notable absence of such effects implies close correspondence of the genomes of the species used in the study. Two cases of possible evolutionary conservation of linkage groups in fishes and mammals were described, involving the G(,6)PD - 6PGD linkage in LG I and the cluster of esterase loci in LG II. One clear case of divergence was observed, that of the linkage of ADA in LG I. It was estimated that a minimum of (TURN)50% of the Xiphophorus genome was marked by the loci studied. Therefore, the prior probability that a new locus will assort independently from the markers already established is estimated to be less than 0.5. A maximum of 21 of the 24 pairs of chromosomes could be marked with at least one locus.^ Only the two LG V loci showed a significant association with a postulated gene controlling the severity of a genetically controlled melanoma caused by abnormal proliferation of macromelanophore pigment pattern cells. The independence of melanotic severity from all other informative markers implies that one or at most a few major genes are involved in control of melanotic severity in this system. ^

Decoding Delay Minimization in Inter-Session Network Coding

Intra-session network coding has been shown to offer significant gains in terms of achievable throughput and delay in settings where one source multicasts data to several clients. In this paper, we consider a more general scenario where multiple sources transmit data to sets of clients over a wireline overlay network. We propose a novel framework for efficient rate allocation in networks where intermediate network nodes have the opportunity to combine packets from different sources using randomized network coding. We formulate the problem as the minimization of the average decoding delay in the client population and solve it with a gradient-based stochastic algorithm. Our optimized inter-session network coding solution is evaluated in different network topologies and is compared with basic intra-session network coding solutions. Our results show the benefits of proper coding decisions and effective rate allocation for lowering the decoding delay when the network is used by concurrent multicast sessions.

SLA-Driven Simulation of Multi-Tenant Scalable Cloud-Distributed Enterprise Information Systems

Cloud Computing is an enabler for delivering large-scale, distributed enterprise applications with strict requirements in terms of performance. It is often the case that such applications have complex scaling and Service Level Agreement (SLA) management requirements. In this paper we present a simulation approach for validating and comparing SLA-aware scaling policies using the CloudSim simulator, using data from an actual Distributed Enterprise Information System (dEIS). We extend CloudSim with concurrent and multi-tenant task simulation capabilities. We then show how different scaling policies can be used for simulating multiple dEIS applications. We present multiple experiments depicting the impact of VM scaling on both datacenter energy consumption and dEIS performance indicators.

Interactive free viewpoint video streaming using prioritized network coding

In free viewpoint applications, the images are captured by an array of cameras that acquire a scene of interest from different perspectives. Any intermediate viewpoint not included in the camera array can be virtually synthesized by the decoder, at a quality that depends on the distance between the virtual view and the camera views available at decoder. Hence, it is beneficial for any user to receive camera views that are close to each other for synthesis. This is however not always feasible in bandwidth-limited overlay networks, where every node may ask for different camera views. In this work, we propose an optimized delivery strategy for free viewpoint streaming over overlay networks. We introduce the concept of layered quality-of-experience (QoE), which describes the level of interactivity offered to clients. Based on these levels of QoE, camera views are organized into layered subsets. These subsets are then delivered to clients through a prioritized network coding streaming scheme, which accommodates for the network and clients heterogeneity and effectively exploit the resources of the overlay network. Simulation results show that, in a scenario with limited bandwidth or channel reliability, the proposed method outperforms baseline network coding approaches, where the different levels of QoE are not taken into account in the delivery strategy optimization.

2014 Doctoral Workshop on Distributed Systems

The Doctoral Workshop on Distributed Systems has been held at Kandersteg, Switzerland, from June 3-5, 2014. Ph.D. students from the Universities of Neuchâtel and Bern as well as the University of Applied Sciences of Fribourg presented their current research work and discussed recent research results. This technical report includes the extended abstracts of the talks given during the workshop.

When small non-coding RNAs meet the ribosome: Tuning the translational machinery

The functions of ribosomes in translation are complex and involve different types of activities critical for decoding the genetic code, linkage of amino acids via amide bonds to form polypeptide chains, as well as the release and proper targeting of the synthesized protein. Non-protein-coding RNAs (ncRNAs) have been recognized to be crucial in establishing regulatory networks.1 However all of the recently discovered ncRNAs involved in translation regulation target the mRNA rather than the ribosome. The main goal of this project is to identify potential novel ncRNAs that directly bind and possibly regulate the ribosome during protein biosynthesis. To address this question we applied various stress conditions to the archaeal model organism Haloferax volcanii and deep-sequenced the ribosome-associated small ncRNA interactome. In total we identified 6.250 ncRNA candidates. Significantly, we observed the emersed presence of tRNA-derived fragments (tRFs). These tRFs have been identified in all domains of life and represent a growing, yet functionally poorly understood, class of ncRNAs. Here we present evidence that tRFs from H. volcanii directly bind to ribosomes. In the presented genomic screen of the ribosome-associated RNome a 26 residue long fragment originating from the 5’ part of valine tRNA was by far the most abundant tRF. The Val-tRF is processed in a stress- dependent manner and was found to primarily target the small ribosomal subunit in vitro and in vivo. As a consequence of ribosome binding, Val-tRF reduces protein synthesis by interfering with peptidyl transferase activity. Therefore this tRF functions as ribosome-bound small ncRNA capable of regulating gene expression in H. volcanii under environmental stress conditions probably by fine-tuning the rate of protein production.2 Currently we are investigating the binding site of this tRF on the 30S subunit in more detail.

Simulation of SLA-based VM-scaling algorithms for cloud-distributed applications

Cloud Computing has evolved to become an enabler for delivering access to large scale distributed applications running on managed network-connected computing systems. This makes possible hosting Distributed Enterprise Information Systems (dEISs) in cloud environments, while enforcing strict performance and quality of service requirements, defined using Service Level Agreements (SLAs). {SLAs} define the performance boundaries of distributed applications, and are enforced by a cloud management system (CMS) dynamically allocating the available computing resources to the cloud services. We present two novel VM-scaling algorithms focused on dEIS systems, which optimally detect most appropriate scaling conditions using performance-models of distributed applications derived from constant-workload benchmarks, together with SLA-specified performance constraints. We simulate the VM-scaling algorithms in a cloud simulator and compare against trace-based performance models of dEISs. We compare a total of three SLA-based VM-scaling algorithms (one using prediction mechanisms) based on a real-world application scenario involving a large variable number of users. Our results show that it is beneficial to use autoregressive predictive SLA-driven scaling algorithms in cloud management systems for guaranteeing performance invariants of distributed cloud applications, as opposed to using only reactive SLA-based VM-scaling algorithms.

Separation of the Ribbon from globally distributed energetic neutral Atom Flux using the first five Years of Ibex Observations

The Interstellar Boundary Explorer (IBEX) observes the IBEX ribbon, which stretches across much of the sky observed in energetic neutral atoms (ENAs). The ribbon covers a narrow (~20°-50°) region that is believed to be roughly perpendicular to the interstellar magnetic field. Superimposed on the IBEX ribbon is the globally distributed flux that is controlled by the processes and properties of the heliosheath. This is a second study that utilizes a previously developed technique to separate ENA emissions in the ribbon from the globally distributed flux. A transparency mask is applied over the ribbon and regions of high emissions. We then solve for the globally distributed flux using an interpolation scheme. Previously, ribbon separation techniques were applied to the first year of IBEX-Hi data at and above 0.71 keV. Here we extend the separation analysis down to 0.2 keV and to five years of IBEX data enabling first maps of the ribbon and the globally distributed flux across the full sky of ENA emissions. Our analysis shows the broadening of the ribbon peak at energies below 0.71 keV and demonstrates the apparent deformation of the ribbon in the nose and heliotail. We show global asymmetries of the heliosheath, including both deflection of the heliotail and differing widths of the lobes, in context of the direction, draping, and compression of the heliospheric magnetic field. We discuss implications of the ribbon maps for the wide array of concepts that attempt to explain the ribbon's origin. Thus, we present the five-year separation of the IBEX ribbon from the globally distributed flux in preparation for a formal IBEX data release of ribbon and globally distributed flux maps to the heliophysics community.